Only code formatting (trailing whitespaces, missing semi-colons, etc...)

Signed-off-by: Yoann Guilhem <yoann.guilhem@esrf.fr>

1_preprocessing/gtSetup.m

@@ -19,7 +19,7 @@ function gtSetup()
 %         Modified fields: match, cryst, xop, acq, seg, rec
 %         Added field    : labgeo, samgeo, version, fsim
 %         Removed fields : geo, opt, match_calib
-%       
+%
 %     Version 008 14-12-2011 by LNervo
 %       Clean code: y/n -> [y/n]
 %                   ';' at the end of lines
@@ -30,7 +30,7 @@ function gtSetup()
 %       Split crystallographic part into functions
 %
 %     Version 006 06-01-2012 by LNervo
-%       Add fed structure 
+%       Add fed structure
 %
 %     Version 005 01-12-2011 by LNervo
 %       Adapt to new parameters file template
@@ -65,12 +65,12 @@ function gtSetup()
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 % title!
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-disp(' ')
-disp(' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~')
-disp(' ~      Welcome to Grain Tracking at the ESRF!      ~')
-disp(' ~                                                  ~')
-disp(' ~     ...using the new parameters template...      ~')
-disp(' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~')
+disp(' ');
+disp(' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~');
+disp(' ~      Welcome to Grain Tracking at the ESRF!      ~');
+disp(' ~                                                  ~');
+disp(' ~     ...using the new parameters template...      ~');
+disp(' ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~');
 pause(1);
 close('all');
 
@@ -80,7 +80,7 @@ if (isempty(whos('global', 'GT_MATLAB_HOME')))
            'your environment is not sane, and you need to either ' ...
            're-initialise or re-run matlab.'])
 end
-global GT_MATLAB_HOME
+global GT_MATLAB_HOME;
 interactive = true;
 
 parameters = [];
@@ -94,17 +94,17 @@ redColor = sprintf(gtGetANSIColour('red'));
 % check for a pre-existing parameters file
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 if exist(fullfile(pwd,'parameters.mat'), 'file')
-    disp('A parameters.mat file already exists in this directory')
-    disp('You can recreate this parameters file to enter new parameters')
-    disp('or use the existing file and just start the correct/undistortion process straightaway')
+    disp('A parameters.mat file already exists in this directory');
+    disp('You can recreate this parameters file to enter new parameters');
+    disp('or use the existing file and just start the correct/undistortion process straightaway');
     load('parameters.mat');
 
     check=inputwdefault('Launch copying without changing parameters? [y/n]', 'n');
     if strcmpi(check, 'y')
-        disp(' ')
+        disp(' ');
         % gtCopyCorrectUndistortWrapper handles condoring of copying
-        disp(' starting data copying using condor')
-        disp(' ')
+        disp(' starting data copying using condor');
+        disp(' ');
         gtCopyCorrectUndistortWrapper(parameters);
         return;
     end
@@ -115,7 +115,7 @@ if exist(fullfile(pwd,'parameters.mat'), 'file')
     if strcmpi(check, 'y')
         parameters = tmppar;
     end
-    clear check tmppar
+    clear check tmppar;
 else
     [parameters, list] = make_parameters(2);
 end
@@ -182,12 +182,12 @@ if exist(parameters_name,'file')
     p=load(parameters_name,'parameters');
     p.parameters.acq.dir = parameters.acq.dir;
     parameters = p.parameters;
-    disp('Using parameters file in the analysis directory...')
-    disp(parameters_name)
-    clear p
+    disp('Using parameters file in the analysis directory...');
+    disp(parameters_name);
+    clear p;
 end
 parameters_name = fullfile(parameters.acq.dir,'parameters.mat');
-clear tmpacqdir
+clear tmpacqdir;
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -196,23 +196,23 @@ clear tmpacqdir
 % check the default names etc before making directories
 % set up directory structure in this location
 
-disp(['setting up directory structure in ' parameters.acq.dir]);
-[~,msg]=mkdir(parameters.acq.dir);                                                disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata') );                        disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata',parameters.acq.name) );    disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata','Orig') );                 disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing') );                  disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','full') );           disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','abs') );            disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','ext') );            disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'2_difspot') );                        disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'3_pairmatching') );                   disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'4_grains') );                         disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'5_reconstruction') );                 disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'6_rendering') );                      disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'7_fed') );                            disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'8_optimization') );                   disp(msg)
-[~,msg]=mkdir( fullfile(parameters.acq.dir,'OAR_log') );                          disp(msg)
+disp(['Setting up directory structure in ' parameters.acq.dir]);
+[~,msg]=mkdir(parameters.acq.dir);                                                disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata') );                        disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata',parameters.acq.name) );    disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'0_rawdata','Orig') );                 disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing') );                  disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','full') );           disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','abs') );            disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'1_preprocessing','ext') );            disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'2_difspot') );                        disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'3_pairmatching') );                   disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'4_grains') );                         disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'5_reconstruction') );                 disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'6_rendering') );                      disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'7_fed') );                            disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'8_optimization') );                   disp(msg);
+[~,msg]=mkdir( fullfile(parameters.acq.dir,'OAR_log') );                          disp(msg);
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -234,14 +234,14 @@ if ~isempty(tmpxml)
     params_xml.energy = tmpxml.acquisition.energy;
     parameters.acq = gtAddMatFile(parameters.acq,params_xml,true,true,false);
 end
-clear params_xml
+clear params_xml;
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Default acquisition parameters 
+% Default acquisition parameters
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 params_acq = gtAcqDefaultParameters(parameters.acq);
 parameters.acq = gtAddMatFile(parameters.acq,params_acq,true,true,false);
-clear params_acq
+clear params_acq;
 
 % now get or confirm the important values:
 if exist(xmlfname,'file')
@@ -268,13 +268,13 @@ if strcmpi(parameters.acq.rotation_axis, 'horizontal')
      parameters.acq = gtModifyStructure(parameters.acq, sublist, 'Images will be rotated for processing:');
 end
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
-clear xmlfname
+clear xmlfname;
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Geometric parameters of setup in Lab reference                  
+% Geometric parameters of setup in Lab reference
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 % get default values for labgeo
@@ -288,7 +288,7 @@ detnorm = cross(parameters.labgeo.detdiru, ...
 parameters.labgeo.detanglemin = minimum;
 parameters.labgeo.detanglemax = maximum;
 
-clear minimum maximum R
+clear minimum maximum R;
 
 header = 'Parameters dealing with arbitrary geometry:';
 % note other fields are calculated, typically during preprocessing when we
@@ -305,11 +305,11 @@ parameters.labgeo = gtModifyStructure(parameters.labgeo, sublist, header);
 % Default voxel size is set to 1 lab unit, so samgeo is like labgeo at
 % omega=0.
 parameters.samgeo = gtGeoSamDefaultParameters();
-    
+
 %header = 'Parameters dealing with arbitrary geometry:';
 %parameters.samgeo = gtModifyStructure(parameters.samgeo, list.samgeo(:,1:2), header);
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -322,15 +322,15 @@ parameters.acq.nof_phases = inputwdefaultnumeric('Number of crystallographic pha
 % get Cryst field information for all phases
 p = make_parameters(2);
 for ii = 1 : parameters.acq.nof_phases
-    
+
     % make a subfolder in 4_grains
-    [~,msg] = mkdir( fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', ii)) );   disp(msg)
+    [~,msg] = mkdir( fullfile(parameters.acq.dir, '4_grains', sprintf('phase_%02d', ii)) );   disp(msg);
     % initialise empty fields
     parameters.xop(ii)   = p.xop;
     parameters.cryst(ii) = p.cryst;
     % fill cryst(ii)
     parameters = gtFillCrystFields(parameters, ii);
-    
+
 end % end crystallography
 
 
@@ -339,7 +339,7 @@ end % end crystallography
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 gtDBConnect();
 try
-    disp(['setting up database tables for ' parameters.acq.name])
+    disp(['setting up database tables for ' parameters.acq.name]);
     gtDBCreateDifblobTable(parameters.acq.name);
     gtDBCreateDifspotTable(parameters.acq.name);
     gtDBCreateExtspotTable(parameters.acq.name);
@@ -358,9 +358,9 @@ catch mexc
         end
     end
 end
-clear check
+clear check;
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -370,10 +370,8 @@ save(parameters_name,'parameters');
 if parameters.acq.no_direct_beam
     % if no direct beam, don't normalise images
     parameters.prep.normalisation = 'none';
-    
 else
     parameters.prep.normalisation = 'margin';
-    
 end
 
 % Andy 26/4/2011 - problem with a scan with 1440/720 images when using default
@@ -412,10 +410,10 @@ parameters.prep.udrift        = [];
 parameters.prep.udriftabs     = [];
 parameters.prep.vdrift        = [];
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
-clear test n test10 test50 dum ind10 ind50
+clear test n test10 test50 dum ind10 ind50;
 
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -423,7 +421,7 @@ clear test n test10 test50 dum ind10 ind50
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 parameters.seg = gtSegDefaultParameters();
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -434,7 +432,7 @@ parameters.match = gtMatchDefaultParametersGUI();
 parameters.match.thetalimits = [parameters.labgeo.detanglemin, ...
                                 parameters.labgeo.detanglemax];
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -443,7 +441,7 @@ save(parameters_name,'parameters');
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 parameters.index = gtIndexDefaultParameters();
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -451,7 +449,7 @@ save(parameters_name,'parameters');
 % FORWARD SIMULATION PARAMETERS
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 parameters.fsim = gtFsimDefaultParameters();
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -459,7 +457,7 @@ save(parameters_name,'parameters');
 % RECONSTRUCTION - parameters
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 parameters.rec = gtRecDefaultParameters();
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
 
 
@@ -472,9 +470,9 @@ parameters.fed.dct_offset    = [0 0 0];
 parameters.fed.renumber_list = [];
 
 
-disp('Saving parameters.mat in the analysis directory...')
+disp('Saving parameters.mat in the analysis directory...');
 save(parameters_name,'parameters');
-disp(' ')
+disp(' ');
 close('all');
 
 
@@ -483,13 +481,13 @@ close('all');
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 check=inputwdefault('Recompile copy function for OAR? Not normally needed! [y/n]', 'n');
 if strcmpi(check,'y')
-    disp('recompiling gtCopyCorrectUndistortCondor')
+    disp('recompiling gtCopyCorrectUndistortCondor');
     gt_mcc('gtCopyCorrectUndistortCondor');
 end
 
-disp(' ')
-disp('Changing to the analysis directory')
-disp(' ')
+disp(' ');
+disp('Changing to the analysis directory');
+disp(' ');
 cd(parameters.acq.dir);
 
 
@@ -498,17 +496,17 @@ cd(parameters.acq.dir);
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 check=inputwdefault('Start copy/move/undistortion process now? [y/n]', 'y');
 if strcmpi(check,'n')
-    disp('You can start the process later by running:')
-    disp('    load(parameters)')
-    disp('    gtCopyCorrectUndistortWrapper(parameters)')
-    return
+    disp('You can start the process later by running:');
+    disp('    load(parameters)');
+    disp('    gtCopyCorrectUndistortWrapper(parameters)');
+    return;
 end
 
 % gtCopyCorrectUndistortWrapper handles oaring of copying
-disp('Starting data copying using OAR')
-disp(' ')
+disp('Starting data copying using OAR');
+disp(' ');
 gtCopyCorrectUndistortWrapper(parameters);
 
-clear msg check
+clear msg check;
 
 end % end of function